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"It's the ordinary Australians that I think aren't getting enough of a guernsey in this conversation.''

Fairfax Media has revealed that university leaders fear up to 160,000 school leavers could be forced to select courses without knowing whether they will pay tens of thousands of dollars in extra fees.

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Dr Spence's intervention into the national debate came as Prime Minister Tony Abbott said during a radio interview that only students who begin university in 2016 would be affected by a deregulation of course fees. Mr Abbott's claim was contradicted by the university sector and the federal education department.

Shortly before thousands of students joined a rally against the education changes in central Sydney, Mr Abbott told ABC radio: "If you start a course under one system you will finish it under one system.

"I want the best students, not only those who can afford to pay": University of Sydney vice-chancellor, Dr Michael Spence. Photo: Tamara Voninski

"If you start next year your conditions of study won't change. It's only for those who start when these changes kick in in 2016 that will have the different conditions applying to them."

But a Department of Education spokesman said: ''Students who enrol in a Commonwealth-supported place after 13 May 2014 will be charged under the existing arrangements until 31 December 2015. After this date they will be charged under the new arrangements.''

This means that a student starting university in 2015 would pay two years of deregulated fees, not three years of capped fees as stated by Mr Abbott.

Australian National University Vice-Chancellor Ian Young said Mr Abbott's comments did not reflect the government's stated policy.

In a television interview on Thursday, Mr Abbott said he could guarantee that university fees would not double because of his government's deregulation of the sector.

But he said students ''would not have to pay a cent upfront''.

''There are lots of things that I can't guarantee, because we live in an uncertain world, but I can guarantee that no one will have to pay a cent upfront because there'll be these fee help loans to cover their up front costs,’’ he told the Nine Network.

Mr Abbott said increased competition in the market would mean some fees go up. ''(But) I suspect others may well put their fees down.''

In an interview with Fairfax Media, Dr Spence said Mr Abbott had provided only a ''partial response'' to question marks over merit-based higher education.

He said he wanted his university to emulate overseas institutions such as Harvard, which has "huge fees", but entry should be based on academic merit only with varying levels of scholarship support to ensure all tiers of society were represented, with wealthier students paying considerably higher fees.

"I don't think social justice requires everyone to pay the same fee [in a deregulated system]. In fact it requires people to pay different amounts depending on their ability to pay. But I think you have to be careful that you don't create a trap where aspirational Australians, not just disadvantaged Australians, will be kept out."

On Wednesday, Dr Spence emailed all staff and students about the proposed changes. The University of Sydney senate, its governing authority, is yet to determine its final position.

He said that the deregulation of undergraduate fees meant that government funding for each Commonwealth-supported student would be cut by an average 20 per cent, and universities would be free to decide their own fees for undergraduate courses.

The government also had reduced its funding for a number of academic disciplines, with modelling showing the university would face cuts of more than $5000 per student in engineering, environmental sciences, communications, and science courses.